The feline major histocompatibility complex (MHC) has been studied for an approach to comparative gene organization of multigene clusters in mammals. We have analyzed sequence diversities of an MHC class II DRB gene(s) in two sister species of the Felidae family, ocelot (Leopardus pardalis) and margay (Leopardus wiedii) in order to study the evolutional history of feline DRB genes. Molecular clones of polymerase chain reaction (PCR)-amplified 238 base pair-DNA segments which encode most the polymorphic beta 2 domain region of the DRB molecule were isolated from 35 ocelot and 26 margay samples collectedfrom 19 geographic locations and 9 countries throughout North, Central and South America. Complete sequence analyses of these clones revealed extremely polymorphic features in both ocelot and margay DRB genes, maintaining 123 alleles in ocelot and 83 alleles in margay. Based on phylogenetic analyses of these sequences along with domestic cat DRB allelic sequences, we have concluded that: (i) both ocelot and margay do not maintain Feca-DRB*01 or *04 lineages found in domestic cat DRB genes; (ii) both ocelot and margay do maintain highly polymorphic Feca-DRB*02 and *03 lineages and less polymorphic *05 lineages; (iii) in addition, both species have unique DRB allelic lineages, i.e., Lepa-DRB*06, *07 and Lewi-DRB*06 lineages; and (iv) existence of species-(sub)specific miniclades, which consist of 2 to 5 allelic sequences appear to suggest rapid evolution of DRB alleles within two to three million years after the split of these two sister species. In order to develop a genetic and physical map of the domestic cat MHC, we have constructed a PAC (P1 artificial chromosome) library from a male domestic cat genomic DNA. Utilizing this library and domestic cat MHC cDNA and PCR clones as probes, we have successfully isolated multiple MHC PAC clones, including a clone which has a DPA region, two clones maintaining a DRA region, one clone with both DRA and DRB regions, and six clones with four class I contigs. Sequence analysis of these clones confirmed MHC genes homologous to the probing sequences and, in addition, other MHC genes, including DNA and DMA genes in the feline MHC class II region.